Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate 5210687 Shew_3115 sodium:dicarboxylate symporter (RefSeq)
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__PV4:5210687 Length = 437 Score = 302 bits (773), Expect = 2e-86 Identities = 158/407 (38%), Positives = 250/407 (61%), Gaps = 3/407 (0%) Query: 11 LTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFIS 70 L+ +I IG+ +G+++G +++ F + + E +GT+F+N + M+VVPLVF+S Sbjct: 22 LSTRIFIGLFSGLILGSIIQYFLADVGFFSGTLVE-VASGLGTMFVNMIMMMVVPLVFVS 80 Query: 71 LVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNA--SLASESMQYS 128 +VCG L + GRLGGKT FY+ T +A+ A++ A+L++PG + + Sbjct: 81 IVCGVLELDDLKSFGRLGGKTFGFYIINTLVAIFAALTVALLLKPGLGVDMTGGTGAEIT 140 Query: 129 AKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDDLN 188 A E P+L +++NIVPSNP+ A + GNMLQ+I A++ G I + + F + N Sbjct: 141 ATELPNLMQLIVNIVPSNPVAAFTSGNMLQVIFMALLVGGVIKAMNGAVPLLQQGFMEGN 200 Query: 189 EVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVYPTLL 248 +++M+++ ++MQLAP GVFALM KL TL SV++Y +++L +LL FVVYP + Sbjct: 201 KLMMKLIGVVMQLAPIGVFALMFKLGATLEASLFLSVVEYLVVILSLLLLWIFVVYPWAV 260 Query: 249 KLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGATI 308 LF+ +S F K ++ LF+ STASSNAT+PVTM +LG VA F +PLGAT+ Sbjct: 261 SLFTPVSAKTFRAKTQEQILFSLSTASSNATIPVTMRTLTEKLGVKRAVAGFGVPLGATM 320 Query: 309 NMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMVLNQ 368 NM G +I +A F+A FG + + ++ + L S+G GVPG G+VM+ ++++Q Sbjct: 321 NMGGVSIYITIAIFFVANSFGAPIAMDQLPALLFSIFLLSVGAGGVPGGGMVMIGVLIHQ 380 Query: 369 VGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEA 415 +GLPVE ++ +DR++DMV T+ NV GD ++ +E A +EA Sbjct: 381 MGLPVEAFVIVAALDRLIDMVLTSCNVVGDAAVLTIVDATENAHDEA 427 Lambda K H 0.325 0.139 0.388 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 427 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 437 Length of database: 437 Length adjustment: 32 Effective length of query: 405 Effective length of database: 405 Effective search space: 164025 Effective search space used: 164025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory